Year of Publication

2016

Degree Name

Doctor of Philosophy (PhD)

Document Type

Doctoral Dissertation

College

Pharmacy

Department

Pharmaceutical Sciences

First Advisor

Dr. Peixuan Guo

Second Advisor

Dr. Robert Lodder

Abstract

Nanopore technology has recently emerged as a new real-time single molecule sensing method. The current dominant technologies, such as mass spectrometry and immunoassay, for protein analysis is still slow and complex, which can’t meet the urgent need and fields of use. Development of a highly simple, portable and sensitive detection system for pathogen detection, disease diagnosis, and environmental monitoring is in great need. Membrane embedded Phi29 connector nanopore, the first protein nanopore coming from bacteriophage, was mainly focusing on DNA and RNA translocation in previous studies. Here, Phi29 connector nanopore was first time established for antibody detection by engineering Epithelial Cell Adhesion Molecule peptide as a probe. The results demonstrate that the specific antibody can be detected in presence of diluted serum or non-specific antibody. To enable detecting more different types of analytes with high sensitivity, developing new nanopore with various properties, such as size, charge, hydrophilic/hydrophobic and physical dimension, is needed. In this work, besides Phi29 nanopore, several new protein nanopores that derived from T3, T4, and SPP1 bacteriophages were developed. A shared property of three step conformational change among these portal channel has been discovered. Elucidating the sequence and oligomeric states of proteins and peptides is critical for understanding their biological functions. Here, SPP1 nanopore was used to characterize the translocation of TAT peptide with dimer and monomer forms. Translocation of the peptide was confirmed by optical single molecule imaging for the first time, and analyzed quantitatively. The dynamics of peptide oligomeric states were clearly differentiated based on their characteristic electronic signatures. Main challenge for probing protein structure, folding, detection and sequencing using nanopore is the ultra-fast translocation speed which normally beyond electronic detection limit. In this work, the peptides translocation was slowed in SPP1 nanopore by changing the charge shielding of the channel. A 500-fold reduction was observed for TAT peptide translocation. By using this method, arginine chain peptide as short as two arginine can be detected first time. Further improving the bandwidth may lead to single amino acid detection and has the potential for protein sequencing. Compared with protein nanopore, de novo designed nanopore can provide numerous advantages, such as tunable size and functionality, ease of construction, scale up and modification. In the final study, an RNA-based biomimetic nanopore was first time constructed. The insertion of RNA nanopore into lipid bilayer and cell membrane were characterized and translocation of short amino acids through RNA nanopore was detected. This new artificial nanopore has the potential to be used for sensing, disease diagnosis, and even protein sequencing.

Digital Object Identifier (DOI)

https://doi.org/10.13023/ETD.2016.428

Available for download on Sunday, November 18, 2018

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